gl2treemix: Converts a genlight object to a treemix input file

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight object to a treemix input file

Description

The output file contains the SNP data in the format expected by treemix – see the treemix manual. The file will be gzipped before in order to be recognised by treemix. Plotting functions provided with treemix will need to be sourced from the treemix download page.

Usage

gl2treemix(
  x,
  outfile = "treemix_input.gz",
  outpath = tempdir(),
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file (including gz extension) [default 'treemix_input.gz'].
outpath	Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() when calling this function or set.tempdir <- getwd() elsewhere in your script to direct output files to your working directory.
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

References

Pickrell and Pritchard (2012). Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genetics https://doi.org/10.1371/journal.pgen.1002967

Examples

gl2treemix(testset.gl, outpath=tempdir())

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.